GapMind for Amino acid biosynthesis

 

Alignments for a candidate for trpD_2 in Paraburkholderia bryophila 376MFSha3.1

Align Anthranilate phosphoribosyltransferase; EC 2.4.2.18 (characterized)
to candidate H281DRAFT_05713 H281DRAFT_05713 anthranilate phosphoribosyltransferase

Query= SwissProt::Q8PD71
         (345 letters)



>FitnessBrowser__Burk376:H281DRAFT_05713
          Length = 343

 Score =  498 bits (1281), Expect = e-145
 Identities = 253/340 (74%), Positives = 286/340 (84%)

Query: 1   MPITPQQALQRTIEHREIFHDEMVDLMRQIMRGEVSDAMVSAILTGLRVKKETIGEIAGA 60
           M ITPQ+ALQRTIEHREIFHDEM+ LMR IMRGE+S  M +AI+TGLRVKKETIGEI  A
Sbjct: 1   MTITPQEALQRTIEHREIFHDEMLHLMRLIMRGELSPVMAAAIITGLRVKKETIGEITAA 60

Query: 61  ATVMREFSRRVEVTDRRHMVDIVGTGGDGSHTFNISTCAMFVAAAGGAKVAKHGNRSVSS 120
           ATVMREF+R VEV D  + VDIVGTGGDGSHTFNIST  MFV+AA GAKVAKHGNR VSS
Sbjct: 61  ATVMREFARHVEVQDNSNFVDIVGTGGDGSHTFNISTATMFVSAAAGAKVAKHGNRGVSS 120

Query: 121 KSGSADALEALGAVIELQPEQVAASLAQTGIGFMYAPVHHPAMKVVAPVRREMGVRTIFN 180
           KSGSAD LEALG  I+LQPEQVAAS+A+TG+GFM+AP HHPAMK +APVRRE+GVRTIFN
Sbjct: 121 KSGSADVLEALGVNIDLQPEQVAASIAETGMGFMFAPNHHPAMKNIAPVRRELGVRTIFN 180

Query: 181 ILGPLTNPAGSPNILMGVFHPDLVGIQARVLQELGAERALVVWGRDGMDELSLGAGTLVG 240
           ILGPLTNPAG+PN LMGVFH DLVGIQ RV+Q LGA+  LVV+G DGMDE+SLGA T VG
Sbjct: 181 ILGPLTNPAGAPNQLMGVFHADLVGIQVRVMQRLGAKHVLVVYGMDGMDEVSLGAATQVG 240

Query: 241 ELRDGQVHEYEVHPEDFGIAMSASRNLKVADAAESRAMLLQVLDNVPGPALDIVALNAGA 300
           ELRDG+V EYE+HPEDFG+ M ++R LKVADA ES+AMLL+ LDN PG A +IV LNAG 
Sbjct: 241 ELRDGEVREYEIHPEDFGMQMVSNRTLKVADATESKAMLLEALDNKPGVAREIVTLNAGT 300

Query: 301 ALYVAGVADSIADGIVRARQVLADGSARACLDAYVAFTQQ 340
           ALY A VA SIA+GI  AR+ +A G ARA +D  + FTQQ
Sbjct: 301 ALYSANVASSIANGIELAREAIASGKARAKVDELIRFTQQ 340


Lambda     K      H
   0.320    0.134    0.377 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 411
Number of extensions: 7
Number of successful extensions: 1
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 345
Length of database: 343
Length adjustment: 29
Effective length of query: 316
Effective length of database: 314
Effective search space:    99224
Effective search space used:    99224
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 49 (23.5 bits)

Align candidate H281DRAFT_05713 H281DRAFT_05713 (anthranilate phosphoribosyltransferase)
to HMM TIGR01245 (trpD: anthranilate phosphoribosyltransferase (EC 2.4.2.18))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.aa/TIGR01245.hmm
# target sequence database:        /tmp/gapView.15013.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01245  [M=330]
Accession:   TIGR01245
Description: trpD: anthranilate phosphoribosyltransferase
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                                    Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
     1e-129  418.5   6.0   1.2e-129  418.4   6.0    1.0  1  lcl|FitnessBrowser__Burk376:H281DRAFT_05713  H281DRAFT_05713 anthranilate pho


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Burk376:H281DRAFT_05713  H281DRAFT_05713 anthranilate phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  418.4   6.0  1.2e-129  1.2e-129       1     329 [.       9     336 ..       9     337 .. 0.99

  Alignments for each domain:
  == domain 1  score: 418.4 bits;  conditional E-value: 1.2e-129
                                    TIGR01245   1 leklldnkdLseeeaeqlmkeimsgeasdaqiaAilvalrvkgeteeeiaglakalrekakkveke 66 
                                                  l++ ++++++ ++e+ +lm+ im+ge+s++  aAi++ lrvk et+ ei+++a+++re a++ve++
  lcl|FitnessBrowser__Burk376:H281DRAFT_05713   9 LQRTIEHREIFHDEMLHLMRLIMRGELSPVMAAAIITGLRVKKETIGEITAAATVMREFARHVEVQ 74 
                                                  578999************************************************************ PP

                                    TIGR01245  67 eseelvDivGTGGDglktiNiSTasalvaaaaGvkvaKhGnrsvssksGsaDvLealgvnlelspe 132
                                                  +++++vDivGTGGDg++t+NiSTa+++v aaaG+kvaKhGnr vssksGsaDvLealgvn++l+pe
  lcl|FitnessBrowser__Burk376:H281DRAFT_05713  75 DNSNFVDIVGTGGDGSHTFNISTATMFVSAAAGAKVAKHGNRGVSSKSGSADVLEALGVNIDLQPE 140
                                                  ****************************************************************** PP

                                    TIGR01245 133 kvarsleevgigFlfAPkyhpalkevapvRkeLgvrtvfNlLGPLlnParaklqvlGvyskdlvev 198
                                                  +va+s++e+g+gF+fAP++hpa+k++apvR+eLgvrt+fN+LGPL+nPa a++q++Gv+++dlv +
  lcl|FitnessBrowser__Burk376:H281DRAFT_05713 141 QVAASIAETGMGFMFAPNHHPAMKNIAPVRRELGVRTIFNILGPLTNPAGAPNQLMGVFHADLVGI 206
                                                  ****************************************************************** PP

                                    TIGR01245 199 laevlknlgvkralvvhgedglDEisltgetkvaelkdgeieeytlspedfglkraeleelkggsa 264
                                                   ++v+++lg+k++lvv g dg+DE+sl + t+v el+dge++ey+++pedfg+++ + + lk+++a
  lcl|FitnessBrowser__Burk376:H281DRAFT_05713 207 QVRVMQRLGAKHVLVVYGMDGMDEVSLGAATQVGELRDGEVREYEIHPEDFGMQMVSNRTLKVADA 272
                                                  ****************************************************************** PP

                                    TIGR01245 265 eenaellkevlegkekkakrdivvlNaaaalyvagkakdlkegvelakeaiksgkalekleelva 329
                                                   e+ ++l e+l +k  + +r+iv lNa++aly a++a+++++g+ela+eai sgka +k++el++
  lcl|FitnessBrowser__Burk376:H281DRAFT_05713 273 TESKAMLLEALDNKP-GVAREIVTLNAGTALYSANVASSIANGIELAREAIASGKARAKVDELIR 336
                                                  **************9.778*****************************************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (330 nodes)
Target sequences:                          1  (343 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 7.78
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory